- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 3de0c1: Fixes pep8 issues from #2386
by GitHub 20 May '16

20 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3de0c16091141aaed22e3a4773877aaa1040a900 https://github.com/galaxyproject/galaxy/commit/3de0c16091141aaed22e3a477387… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Fixes pep8 issues from #2386 Commit: 389fa8ad7da8a82dd3bacdf52a7914aee889a112 https://github.com/galaxyproject/galaxy/commit/389fa8ad7da8a82dd3bacdf52a79… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #2392 from galaxyproject/fix_pep8 Fixes pep8 issues from #2386 Compare: https://github.com/galaxyproject/galaxy/compare/a743e530d09f...389fa8ad7da8

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[galaxyproject/galaxy] 3de0c1: Fixes pep8 issues from #2386
by GitHub 20 May '16

20 May '16

Branch: refs/heads/fix_pep8 Home: https://github.com/galaxyproject/galaxy Commit: 3de0c16091141aaed22e3a4773877aaa1040a900 https://github.com/galaxyproject/galaxy/commit/3de0c16091141aaed22e3a477387… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Fixes pep8 issues from #2386

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[galaxyproject/ansible-pulsar]
by GitHub 20 May '16

20 May '16

Branch: refs/tags/0.4.2 Home: https://github.com/galaxyproject/ansible-pulsar

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[galaxyproject/ansible-pulsar] a5759d: Additional configurability, especially for uWSGI
by GitHub 20 May '16

20 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-pulsar Commit: a5759d31a3f49bfc1ee7dc54437c845080231fd0 https://github.com/galaxyproject/ansible-pulsar/commit/a5759d31a3f49bfc1ee7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M README.md M defaults/main.yml M tasks/main.yml M templates/server.ini.j2 Log Message: ----------- Additional configurability, especially for uWSGI

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[galaxyproject/galaxy] 308f74: Ever more informative, explicit, and complete rele...
by GitHub 20 May '16

20 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 308f74a25a5e7d4212f3b5644b312fe5e38139d8 https://github.com/galaxyproject/galaxy/commit/308f74a25a5e7d4212f3b5644b31… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Ever more informative, explicit, and complete release checklist. - Update announcement acitivties to reflect release notes handled by devs in a diffrent, earlier step. - Add example post links for various announcement activities. - Add credential location information for Twitter. - Add branch-time item to update bioblend target testing. - Add item for scheduling a committer priority meeting (as done for this release by @martenson - thanks for taking charge on that!). Commit: a743e530d09fc41b98c2e796ccd37fb27bbe3125 https://github.com/galaxyproject/galaxy/commit/a743e530d09fc41b98c2e796ccd3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #2388 from jmchilton/bootstrap_history_somemore Ever more informative, explicit, and complete release checklist. Compare: https://github.com/galaxyproject/galaxy/compare/4f3e0f6d4057...a743e530d09f

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[galaxyproject/galaxy] a547fe: Docker swarm support for interactive environments
by GitHub 20 May '16

20 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a547feb9a035c1234bf1e3e506e946f4da3619e8 https://github.com/galaxyproject/galaxy/commit/a547feb9a035c1234bf1e3e506e9… Author: James Taylor <james(a)jamestaylor.org> Date: 2016-05-19 (Thu, 19 May 2016) Changed paths: M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Docker swarm support for interactive environments Commit: 49b9f8128b4eb8688f416aefd33f922353cc6309 https://github.com/galaxyproject/galaxy/commit/49b9f8128b4eb8688f416aefd33f… Author: James Taylor <james(a)jamestaylor.org> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Support Docker Swarm without a configuration parameter Commit: 4f3e0f6d4057848f299f5b10a4e66eb4c0855071 https://github.com/galaxyproject/galaxy/commit/4f3e0f6d4057848f299f5b10a4e6… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #2386 from jxtx/gies-swarm Docker swarm support for interactive environments Compare: https://github.com/galaxyproject/galaxy/compare/288498ac84a4...4f3e0f6d4057

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[galaxyproject/galaxy] ad3a65: remove the comment that breaks toc generation
by GitHub 20 May '16

20 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: ad3a65a6881712b7dcd7e44ca55a6529144e4080 https://github.com/galaxyproject/galaxy/commit/ad3a65a6881712b7dcd7e44ca55a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M doc/source/releases/index.rst Log Message: ----------- remove the comment that breaks toc generation Commit: d926b3f5099cb0f3153126a59d3a07374e486c80 https://github.com/galaxyproject/galaxy/commit/d926b3f5099cb0f3153126a59d3a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M doc/source/releases/index.rst Log Message: ----------- Merge pull request #2373 from martenson/fix=release-docs [16.04] remove the comment that breaks toc generation Commit: 5f8b9e04baf78f5a4009afc07184327b58b247d3 https://github.com/galaxyproject/galaxy/commit/5f8b9e04baf78f5a4009afc07184… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-19 (Thu, 19 May 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Remove stray print left in workflow sharing which actually throws an exception and breaks sharing when item_name is unicode. Commit: e194c64e262592018429c07ffae931899f130a28 https://github.com/galaxyproject/galaxy/commit/e194c64e262592018429c07ffae9… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-05-19 (Thu, 19 May 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Merge pull request #2377 from dannon/stray_print_breaking_sharing [16.04] Remove stray print left in workflow sharing which actually throws an … Commit: 8d0e1c51df31fa862baac815e24170cceeebb5da https://github.com/galaxyproject/galaxy/commit/8d0e1c51df31fa862baac815e241… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Fix Pulsar remote metadata temp files for https://github.com/galaxyproject/galaxy/pull/1688/commits/a2e31403753c407e7… xref #1688 and https://github.com/galaxyproject/galaxy/commit/2a90811ea37e1361d58538f11500… Commit: ac5a328e5f56d395940e29532facc5655f79d8fe https://github.com/galaxyproject/galaxy/commit/ac5a328e5f56d395940e29532fac… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M doc/source/releases/index.rst M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Merge branch 'release_16.04' Compare: https://github.com/galaxyproject/galaxy/compare/f730f2d1abff...ac5a328e5f56

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[galaxyproject/galaxy] 8d0e1c: Fix Pulsar remote metadata temp files for https://...
by GitHub 20 May '16

20 May '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 8d0e1c51df31fa862baac815e24170cceeebb5da https://github.com/galaxyproject/galaxy/commit/8d0e1c51df31fa862baac815e241… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Fix Pulsar remote metadata temp files for https://github.com/galaxyproject/galaxy/pull/1688/commits/a2e31403753c407e7… xref #1688 and https://github.com/galaxyproject/galaxy/commit/2a90811ea37e1361d58538f11500…

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[galaxyproject/galaxy] 17e829: add edam_data infrastructure to the Galaxy datatyp...
by GitHub 20 May '16

20 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 17e82957af9d4a586ee8262f0fb6e98041d436f5 https://github.com/galaxyproject/galaxy/commit/17e82957af9d4a586ee8262f0fb6… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/registry.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- add edam_data infrastructure to the Galaxy datatypes Commit: 8a2b08096ad197df229df8f77eeeed2c4d3e5068 https://github.com/galaxyproject/galaxy/commit/8a2b08096ad197df229df8f77eee… Author: Hervé Ménager <herve.menager(a)gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- add basic EDAM data metadata for data.py datatypes Based on agreement with bgruening, jongithub, and fmareuil on the annotation of datatypes with EDAM data concepts. Commit: 5714c85a79d88d4efddcc30f414d376be9a79306 https://github.com/galaxyproject/galaxy/commit/5714c85a79d88d4efddcc30f414d… Author: Hervé Ménager <herve.menager(a)gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- add basic EDAM data metadata for sequence.py datatypes Based on agreement with bgruening, jongithub, and fmareuil on the annotation of datatypes with EDAM data concepts. Commit: 98e33d0b525db1ce3d7a66e7ee2d8fb63798d366 https://github.com/galaxyproject/galaxy/commit/98e33d0b525db1ce3d7a66e7ee2d… Author: Hervé Ménager <herve.menager(a)gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/assembly.py Log Message: ----------- add EDAM data/formats to assembly datatypes Commit: 4ebeb548fdea3d157b62cae7a6e613e7821e292d https://github.com/galaxyproject/galaxy/commit/4ebeb548fdea3d157b62cae7a6e6… Author: Hervé Ménager <hmenager(a)pasteur.fr> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/xml.py Log Message: ----------- add EDAM format and data for Phylo XML Commit: 907950df803e881bbefc4bf16ad8e9a0cff5725d https://github.com/galaxyproject/galaxy/commit/907950df803e881bbefc4bf16ad8… Author: Hervé Ménager <hmenager(a)pasteur.fr> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/triples.py Log Message: ----------- complete EDAM annotations for triple datatypes. Commit: c0867c665306bc59d8353a3fb192f49c87bbd7d7 https://github.com/galaxyproject/galaxy/commit/c0867c665306bc59d8353a3fb192… Author: Hervé Ménager <hmenager(a)pasteur.fr> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/tracks.py Log Message: ----------- complete EDAM annotations for Gene track format Commit: 0002eac91fa644e22aa5b939405e6e4801239384 https://github.com/galaxyproject/galaxy/commit/0002eac91fa644e22aa5b939405e… Author: Hervé Ménager <hmenager(a)pasteur.fr> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- complete EDAM annotations in text datatypes. Commit: 425cee668d3d0ab2b0f4912aabb370b600218199 https://github.com/galaxyproject/galaxy/commit/425cee668d3d0ab2b0f4912aabb3… Author: Hervé Ménager <hmenager(a)pasteur.fr> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/qualityscore.py Log Message: ----------- add EDAM annotations to quality datatypes. Commit: c69aa8b54923b2df4ad6b7a430459a6767fb8f27 https://github.com/galaxyproject/galaxy/commit/c69aa8b54923b2df4ad6b7a43045… Author: Hervé Ménager <hmenager(a)pasteur.fr> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/proteomics.py Log Message: ----------- add EDAM annotation to proteomics datatypes Commit: 0511d72e4a14e8d0c357733564f1ad6cea649723 https://github.com/galaxyproject/galaxy/commit/0511d72e4a14e8d0c357733564f1… Author: Hervé Ménager <hmenager(a)pasteur.fr> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/msa.py Log Message: ----------- add EDAM annotations to msa datatypes. Commit: 2a7436eb630d79072b8f1c4a80ccf1262a195cef https://github.com/galaxyproject/galaxy/commit/2a7436eb630d79072b8f1c4a80cc… Author: Hervé Ménager <hmenager(a)pasteur.fr> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- add EDAM annotations to interval datatypes. Commit: ec7519b267229ae4c13c6687332d3bb6e467718b https://github.com/galaxyproject/galaxy/commit/ec7519b267229ae4c13c6687332d… Author: Hervé Ménager <hmenager(a)pasteur.fr> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/images.py Log Message: ----------- add EDAM annotations to image datatypes. Commit: 6929cd4cd15e176054bec286c440ca7f97589efe https://github.com/galaxyproject/galaxy/commit/6929cd4cd15e176054bec286c440… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/text.py Log Message: ----------- Address review comments by @nsoranzo Commit: 50fe4914339ac6c1f2a80c87eb4ee89967db9297 https://github.com/galaxyproject/galaxy/commit/50fe4914339ac6c1f2a80c87eb4e… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/api/datatypes.py Log Message: ----------- Fix PEP8 for biotools PR Commit: 2a5b04075cd3d3f467c58f2ef134088931725d6f https://github.com/galaxyproject/galaxy/commit/2a5b04075cd3d3f467c58f2ef134… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/images.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Fix some review comments Commit: 9460e6ea4910d086409419b5e17a2ce34da0f15a https://github.com/galaxyproject/galaxy/commit/9460e6ea4910d086409419b5e17a… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/xml.py Log Message: ----------- More constistent ordering. Remove some blank lines Commit: 1b7c4395e279903a13f61c0789dd868628fc943f https://github.com/galaxyproject/galaxy/commit/1b7c4395e279903a13f61c0789dd… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/tracks.py M lib/galaxy/datatypes/triples.py M lib/galaxy/datatypes/xml.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #2387 from nsoranzo/edam_data Add support for EDAM data annotations to datatypes Compare: https://github.com/galaxyproject/galaxy/compare/b6f8e1c7996c...1b7c4395e279

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[galaxyproject/galaxy] ad3a65: remove the comment that breaks toc generation
by GitHub 20 May '16

20 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ad3a65a6881712b7dcd7e44ca55a6529144e4080 https://github.com/galaxyproject/galaxy/commit/ad3a65a6881712b7dcd7e44ca55a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M doc/source/releases/index.rst Log Message: ----------- remove the comment that breaks toc generation Commit: d926b3f5099cb0f3153126a59d3a07374e486c80 https://github.com/galaxyproject/galaxy/commit/d926b3f5099cb0f3153126a59d3a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M doc/source/releases/index.rst Log Message: ----------- Merge pull request #2373 from martenson/fix=release-docs [16.04] remove the comment that breaks toc generation Commit: 5f8b9e04baf78f5a4009afc07184327b58b247d3 https://github.com/galaxyproject/galaxy/commit/5f8b9e04baf78f5a4009afc07184… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-19 (Thu, 19 May 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Remove stray print left in workflow sharing which actually throws an exception and breaks sharing when item_name is unicode. Commit: e194c64e262592018429c07ffae931899f130a28 https://github.com/galaxyproject/galaxy/commit/e194c64e262592018429c07ffae9… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-05-19 (Thu, 19 May 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Merge pull request #2377 from dannon/stray_print_breaking_sharing [16.04] Remove stray print left in workflow sharing which actually throws an … Commit: b6f8e1c7996cdd86e286a7f3f6af62f247428e3a https://github.com/galaxyproject/galaxy/commit/b6f8e1c7996cdd86e286a7f3f6af… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-19 (Thu, 19 May 2016) Changed paths: M doc/source/releases/index.rst Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/eb430f4078d4...b6f8e1c7996c

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[galaxyproject/galaxy] c453d7: With the removal of Python 2.6 support, the backpo...
by GitHub 20 May '16

20 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c453d742effb5bb619c7b8b25181b5967c75c3a4 https://github.com/galaxyproject/galaxy/commit/c453d742effb5bb619c7b8b25181… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-19 (Thu, 19 May 2016) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt R lib/galaxy/util/backports/importlib/__init__.py M lib/galaxy/web/framework/webapp.py Log Message: ----------- With the removal of Python 2.6 support, the backport of importlib and ordereddict are no longer necessary. Commit: 2b489df04cac987a1e88948fca2df702fedc429a https://github.com/galaxyproject/galaxy/commit/2b489df04cac987a1e88948fca2d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-19 (Thu, 19 May 2016) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- Remove import of unused sys.version_info Commit: eb430f4078d496ed020262a7fcddf3094da98680 https://github.com/galaxyproject/galaxy/commit/eb430f4078d496ed020262a7fcdd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-19 (Thu, 19 May 2016) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt R lib/galaxy/util/backports/importlib/__init__.py M lib/galaxy/web/framework/webapp.py Log Message: ----------- Merge pull request #2380 from natefoo/remove-py26-deps Remove backported importlib and ordereddict Compare: https://github.com/galaxyproject/galaxy/compare/55c0de689167...eb430f4078d4

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[galaxyproject/galaxy] 49cb1d: Note on updating tool testing
by GitHub 19 May '16

19 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 49cb1d6a0ab5e1c57eeb1878ad831c8e40914673 https://github.com/galaxyproject/galaxy/commit/49cb1d6a0ab5e1c57eeb1878ad83… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-05-19 (Thu, 19 May 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Note on updating tool testing Commit: d1e07e989d32c781344b0c198e96fc172bb74386 https://github.com/galaxyproject/galaxy/commit/d1e07e989d32c781344b0c198e96… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-05-19 (Thu, 19 May 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Add devteam Commit: 55c0de689167b2335789d91650c106eda560b31e https://github.com/galaxyproject/galaxy/commit/55c0de689167b2335789d91650c1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-19 (Thu, 19 May 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #2381 from erasche/from-iuc-764 Note on updating tool testing Compare: https://github.com/galaxyproject/galaxy/compare/b44e284be3ed...55c0de689167

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[galaxyproject/galaxy]
by GitHub 19 May '16

19 May '16

Branch: refs/heads/docker_release Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] 6e6bfc: Update template to include the release of the Dock...
by GitHub 19 May '16

19 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6e6bfc796d0aa6a7c795debe2be43e82b949590a https://github.com/galaxyproject/galaxy/commit/6e6bfc796d0aa6a7c795debe2be4… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-05-19 (Thu, 19 May 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Update template to include the release of the Docker container Commit: b44e284be3ed15a3fb3bb77bfac07110ad4ce96d https://github.com/galaxyproject/galaxy/commit/b44e284be3ed15a3fb3bb77bfac0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-19 (Thu, 19 May 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #2378 from galaxyproject/docker_release Update template to include the release of the Docker container Compare: https://github.com/galaxyproject/galaxy/compare/8cdc1244ef34...b44e284be3ed

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[galaxyproject/galaxy] 6e6bfc: Update template to include the release of the Dock...
by GitHub 19 May '16

19 May '16

Branch: refs/heads/docker_release Home: https://github.com/galaxyproject/galaxy Commit: 6e6bfc796d0aa6a7c795debe2be43e82b949590a https://github.com/galaxyproject/galaxy/commit/6e6bfc796d0aa6a7c795debe2be4… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-05-19 (Thu, 19 May 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Update template to include the release of the Docker container

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[galaxyproject/galaxy] ad3a65: remove the comment that breaks toc generation
by GitHub 18 May '16

18 May '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: ad3a65a6881712b7dcd7e44ca55a6529144e4080 https://github.com/galaxyproject/galaxy/commit/ad3a65a6881712b7dcd7e44ca55a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M doc/source/releases/index.rst Log Message: ----------- remove the comment that breaks toc generation Commit: d926b3f5099cb0f3153126a59d3a07374e486c80 https://github.com/galaxyproject/galaxy/commit/d926b3f5099cb0f3153126a59d3a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M doc/source/releases/index.rst Log Message: ----------- Merge pull request #2373 from martenson/fix=release-docs [16.04] remove the comment that breaks toc generation Compare: https://github.com/galaxyproject/galaxy/compare/99c8f54a77c4...d926b3f5099c

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[galaxyproject/galaxy] 2ddf4e: Upgrade shared ui libraries, add test cases
by GitHub 18 May '16

18 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2ddf4e02fc6e8ee1cb28b1cf78146efe0a8e16ab https://github.com/galaxyproject/galaxy/commit/2ddf4e02fc6e8ee1cb28b1cf7814… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js R client/galaxy/scripts/mvc/tool/tool-template.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/ui.less M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/utils/utils.js M static/style/blue/base.css M test/qunit/test-app.js M test/qunit/test-data/fakeserver.js M test/qunit/tests/form_tests.js M test/qunit/tests/modal_tests.js M test/qunit/tests/ui_tests.js Log Message: ----------- Upgrade shared ui libraries, add test cases Commit: 8cdc1244ef3470df5c53cc8c1147575a56388216 https://github.com/galaxyproject/galaxy/commit/8cdc1244ef3470df5c53cc8c1147… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js R client/galaxy/scripts/mvc/tool/tool-template.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/ui.less M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/utils/utils.js M static/style/blue/base.css M test/qunit/test-app.js M test/qunit/test-data/fakeserver.js M test/qunit/tests/form_tests.js M test/qunit/tests/modal_tests.js M test/qunit/tests/ui_tests.js Log Message: ----------- Merge pull request #2368 from guerler/revise_ui_001 Upgrade shared ui libraries, add test cases Compare: https://github.com/galaxyproject/galaxy/compare/702fe3c11218...8cdc1244ef34

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[galaxyproject/galaxy] 5a8d2a: More clarification of release process.
by GitHub 18 May '16

18 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5a8d2a1ad8b70c86f6fd57fd31337e82c0e7ee3f https://github.com/galaxyproject/galaxy/commit/5a8d2a1ad8b70c86f6fd57fd3133… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M Makefile M scripts/bootstrap_history.py Log Message: ----------- More clarification of release process. Commit: 702fe3c11218d6a44b8b07379e9e980a672c9c12 https://github.com/galaxyproject/galaxy/commit/702fe3c11218d6a44b8b07379e9e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M Makefile M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #2372 from jmchilton/release_process_revise_again More clarification of release process. Compare: https://github.com/galaxyproject/galaxy/compare/978fec055ef8...702fe3c11218

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[galaxyproject/galaxy] ed4132: Python3: Use open() instead of file()
by GitHub 18 May '16

18 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ed4132d9c0c94baa38e289b43aa08c1c42b81083 https://github.com/galaxyproject/galaxy/commit/ed4132d9c0c94baa38e289b43aa0… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/runners/__init__.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py M lib/tool_shed/util/tool_util.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py M test/base/twilltestcase.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_0060_workflows.py M test/shed_functional/functional/test_0100_complex_repository_dependencies.py M test/shed_functional/functional/test_0170_complex_prior_installation_required.py M test/shed_functional/functional/test_0300_reset_all_metadata.py M test/shed_functional/functional/test_0310_hg_api_features.py M test/shed_functional/functional/test_1060_install_repository_with_workflow.py M test/shed_functional/functional/test_1120_install_repository_with_complex_dependencies.py M test/shed_functional/functional/test_1190_complex_prior_installation_required.py M test/shed_functional/functional/test_1300_reset_all_metadata.py M test/shed_functional/functional/test_1420_tool_dependency_environment_inheritance.py M test/shed_functional/functional_tests.py M tools/data_source/microbial_import.py M tools/extract/extract_genomic_dna.py M tools/filters/axt_to_lav.py M tools/filters/bed_to_gff_converter.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff_to_bed_converter.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/joinWrapper.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/stats/filtering.py M tools/stats/gsummary.py Log Message: ----------- Python3: Use open() instead of file() Commit: 8a43b2b492e6282a67cc7e8279cc727d5de26dc2 https://github.com/galaxyproject/galaxy/commit/8a43b2b492e6282a67cc7e8279cc… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M contrib/nagios/check_galaxy.py M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py M lib/galaxy/model/migrate/versions/0057_request_notify.py M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py M scripts/api/upload_to_history.py M scripts/check_galaxy.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/data_libraries/build_whoosh_index.py M scripts/drmaa_external_killer.py M scripts/drmaa_external_runner.py M scripts/extract_dataset_part.py M scripts/microbes/harvest_bacteria.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/tool_shed/api/common.py M scripts/tool_shed/api/create_categories.py M scripts/tool_shed/api/create_users.py M scripts/tool_shed/api/import_capsule.py M scripts/tool_shed/api/reset_metadata_on_repositories.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tools/maf/check_loc_file.py M scripts/transfer.py M test/base/asserts/__init__.py M test/base/asserts/xml.py M test/base/driver_util.py M test/base/twilltestcase.py M test/casperjs/casperjs_runner.py M test/casperjs/server_env.py M test/functional/test_data_managers.py M test/functional/test_toolbox.py M test/shed_functional/base/twilltestcase.py M test/unit/tools/test_execution.py M test/unit/tools/test_select_parameters.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M tools/data_source/data_source.py M tools/data_source/fetch.py M tools/data_source/hbvar_filter.py M tools/data_source/upload.py M tools/evolution/add_scores.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/lav_to_bed.py M tools/filters/sff_extract.py M tools/filters/sorter.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_split_by_species.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/solid_tools/maq_cs_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py Log Message: ----------- Python 3: use "as" instead of comma in except clause Commit: 6ba6f798ecfae5d7a30d50de785075ffa7bfb844 https://github.com/galaxyproject/galaxy/commit/6ba6f798ecfae5d7a30d50de7850… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M contrib/nagios/check_galaxy.py M cron/build_chrom_db.py M lib/galaxy/security/__init__.py M lib/galaxy/util/directory_hash.py M lib/galaxy_utils/sequence/vcf.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/migrate/common.py M lib/tool_shed/metadata/metadata_generator.py M scripts/api/data_manager_example_execute.py M scripts/api/search.py M scripts/api/upload_to_history.py M scripts/check_galaxy.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/populate_uuid.py M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/data_libraries/build_lucene_index.py M scripts/data_libraries/build_whoosh_index.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/harvest_bacteria.py M scripts/runtime_stats.py M scripts/tool_shed/build_ts_whoosh_index.py M test/api/test_datasets.py M test/base/driver_util.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HistoryManager.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py M test/unit/web/framework/test_webapp.py M tools/extract/extract_genomic_dna.py M tools/filters/join.py M tools/filters/mergeCols.py M tools/filters/sff_extract.py M tools/genomespace/genomespace_file_browser.py M tools/metag_tools/shrimp_wrapper.py M tools/ngs_simulation/ngs_simulation.py M tools/phenotype_association/pagetag.py M tools/stats/gsummary.py Log Message: ----------- Fix more E203 flake8 errors Commit: 978fec055ef817e008252002ea956f9d304d51c3 https://github.com/galaxyproject/galaxy/commit/978fec055ef817e008252002ea95… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M contrib/nagios/check_galaxy.py M cron/build_chrom_db.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py M lib/galaxy/model/migrate/versions/0057_request_notify.py M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py M lib/galaxy/security/__init__.py M lib/galaxy/util/directory_hash.py M lib/galaxy_utils/sequence/vcf.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/migrate/common.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/tool_util.py M scripts/api/data_manager_example_execute.py M scripts/api/search.py M scripts/api/upload_to_history.py M scripts/check_galaxy.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/data_libraries/build_lucene_index.py M scripts/data_libraries/build_whoosh_index.py M scripts/drmaa_external_killer.py M scripts/drmaa_external_runner.py M scripts/extract_dataset_part.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/harvest_bacteria.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/runtime_stats.py M scripts/tool_shed/api/common.py M scripts/tool_shed/api/create_categories.py M scripts/tool_shed/api/create_users.py M scripts/tool_shed/api/import_capsule.py M scripts/tool_shed/api/reset_metadata_on_repositories.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tools/maf/check_loc_file.py M scripts/transfer.py M test/api/test_datasets.py M test/base/asserts/__init__.py M test/base/asserts/xml.py M test/base/driver_util.py M test/base/twilltestcase.py M test/casperjs/casperjs_runner.py M test/casperjs/server_env.py M test/functional/test_data_managers.py M test/functional/test_toolbox.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_0060_workflows.py M test/shed_functional/functional/test_0100_complex_repository_dependencies.py M test/shed_functional/functional/test_0170_complex_prior_installation_required.py M test/shed_functional/functional/test_0300_reset_all_metadata.py M test/shed_functional/functional/test_0310_hg_api_features.py M test/shed_functional/functional/test_1060_install_repository_with_workflow.py M test/shed_functional/functional/test_1120_install_repository_with_complex_dependencies.py M test/shed_functional/functional/test_1190_complex_prior_installation_required.py M test/shed_functional/functional/test_1300_reset_all_metadata.py M test/shed_functional/functional/test_1420_tool_dependency_environment_inheritance.py M test/shed_functional/functional_tests.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HistoryManager.py M test/unit/tools/test_execution.py M test/unit/tools/test_select_parameters.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py M test/unit/web/framework/test_webapp.py M tools/data_source/data_source.py M tools/data_source/fetch.py M tools/data_source/hbvar_filter.py M tools/data_source/microbial_import.py M tools/data_source/upload.py M tools/evolution/add_scores.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_lav.py M tools/filters/bed_to_gff_converter.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff_to_bed_converter.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/lav_to_bed.py M tools/filters/mergeCols.py M tools/filters/sff_extract.py M tools/filters/sorter.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_split_by_species.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py Log Message: ----------- Merge pull request #2370 from nsoranzo/python3 Python3: use open() instead of file() Compare: https://github.com/galaxyproject/galaxy/compare/5a15bd0a00a6...978fec055ef8

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[galaxyproject/galaxy] 35a716: Not all objects added to the runner work queue are
by GitHub 18 May '16

18 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 35a716b8549bd575c96ef9cafe0e78a7e2048139 https://github.com/galaxyproject/galaxy/commit/35a716b8549bd575c96ef9cafe0e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Not all objects added to the runner work queue are JobWrappers/TaskWrappers as claimed in the comment. AsynchronousJobStates could also be added, and if the fail method was called this would result in the AttributeError of attempting to access an AJS' non-existent `get_id_tag` being logged in job.exeception as a red herring. Commit: d8430e5c4b6c5d8dd18fed6846f6f30d4a97e0eb https://github.com/galaxyproject/galaxy/commit/d8430e5c4b6c5d8dd18fed6846f6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: A doc/source/releases/16.04.rst M doc/source/releases/16.04_announce.rst A doc/source/releases/16.07_announce.rst M doc/source/releases/index.rst Log Message: ----------- generated notes with basic manual curation Commit: 93d1d5611e3d62f928af49edd884dfea5fcf4c11 https://github.com/galaxyproject/galaxy/commit/93d1d5611e3d62f928af49edd884… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- add deprecation notices Commit: 40e596f26479e14b66b71842cee779e46a882047 https://github.com/galaxyproject/galaxy/commit/40e596f26479e14b66b71842cee7… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- Update 16.04_announce.rst Added more deprecations from #1757 Commit: 86127cdfdd7140e167a54622b83e09e616dbbe9a https://github.com/galaxyproject/galaxy/commit/86127cdfdd7140e167a54622b83e… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- Update 16.04_announce.rst Fix my rst syntax. Commit: e0a9efc307ac9f3a7a36c724684b16802cd6d31b https://github.com/galaxyproject/galaxy/commit/e0a9efc307ac9f3a7a36c724684b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M doc/source/releases/16.04.rst M doc/source/releases/16.04_announce.rst Log Message: ----------- include security note for hg upgrade; some reordering Commit: edbc82c215e87a5962ed740d97c352931b9402c0 https://github.com/galaxyproject/galaxy/commit/edbc82c215e87a5962ed740d97c3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- Merge branch '16.04_release_notes' of https://github.com/martenson/galaxy into 16.04_release_notes Conflicts: doc/source/releases/16.04_announce.rst Commit: 633162c7f558f1bc3bfaaa54dde3c7fc4156c190 https://github.com/galaxyproject/galaxy/commit/633162c7f558f1bc3bfaaa54dde3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- fix wrong merge Commit: 65e1d68efd2a1bc83e340a8419f55f95a440c6c3 https://github.com/galaxyproject/galaxy/commit/65e1d68efd2a1bc83e340a8419f5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- typo Commit: db5c0d95f6e10a5a723bc4bb54c11597ed629e9c https://github.com/galaxyproject/galaxy/commit/db5c0d95f6e10a5a723bc4bb54c1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M doc/source/releases/16.04.rst Log Message: ----------- reorde notes a bit more based on impact/importance Commit: b85d604e30809d7e6b73f4762189182e7e82416b https://github.com/galaxyproject/galaxy/commit/b85d604e30809d7e6b73f4762189… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-13 (Fri, 13 May 2016) Changed paths: M doc/source/releases/16.01.rst M doc/source/releases/16.04.rst Log Message: ----------- Move some PRs that were merged in 16.01 before its release Galaxy 16.01 was officially released on 2016/02/24. Commit: c516c9fd45ffda5d4d74497bc96efc51966fdd22 https://github.com/galaxyproject/galaxy/commit/c516c9fd45ffda5d4d74497bc96e… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-13 (Fri, 13 May 2016) Changed paths: M doc/source/releases/16.04.rst Log Message: ----------- Fix truncated PR titles and some acknowledgements Commit: dc5a5eb2eb1af48e14234d42aa8cacd3fd1aba1e https://github.com/galaxyproject/galaxy/commit/dc5a5eb2eb1af48e14234d42aa8c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-13 (Fri, 13 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- Add Bitbucket deprecation details Commit: 76fb9b72c34ecd6bead61b372a32dc0bd24375eb https://github.com/galaxyproject/galaxy/commit/76fb9b72c34ecd6bead61b372a32… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-13 (Fri, 13 May 2016) Changed paths: M doc/source/releases/16.04.rst Log Message: ----------- Add some missing PRs and merge some entries Commit: 38209bbbac705612c11f7f3083e357e046cb5c64 https://github.com/galaxyproject/galaxy/commit/38209bbbac705612c11f7f3083e3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-14 (Sat, 14 May 2016) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Merge pull request #2350 from natefoo/fix-ajs-red-herring [16.04] Properly handle AsynchronousJobState objects in the job runner work queue Commit: 2390da54aec143358767e7977cffc70d040b04b5 https://github.com/galaxyproject/galaxy/commit/2390da54aec143358767e7977cff… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Fix for slurm's complete_terminal_job where if unable to inspect the failed job with scontrol drmaajobrunner's _complete_terminal_job was called twice. Commit: 3b7f6cb7777cf2a92d17928b38abe13bd3cdb338 https://github.com/galaxyproject/galaxy/commit/3b7f6cb7777cf2a92d17928b38ab… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- add some highlights, seems tough for this release Commit: 62b6eaa92aac9520f12968cb41690692c8c3fa4f https://github.com/galaxyproject/galaxy/commit/62b6eaa92aac9520f12968cb4169… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M doc/source/releases/16.01.rst M doc/source/releases/16.04.rst M doc/source/releases/16.04_announce.rst Log Message: ----------- Merge branch '16.04_release_notes' of https://github.com/martenson/galaxy into 16.04_release_notes Commit: cc86096c83b5835e40e034611ad64bf3827e5c6d https://github.com/galaxyproject/galaxy/commit/cc86096c83b5835e40e034611ad6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #2362 from dannon/slurm_complete_job_fix [16.04] Fix for slurm's complete_terminal_job where if unable to inspect the … Commit: afb9027482f3a98a2b6d9e9fd049ded1da78c666 https://github.com/galaxyproject/galaxy/commit/afb9027482f3a98a2b6d9e9fd049… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- final touch of release notes from my side Commit: 50e596fb1b540a69f785296921a2611566a5b12b https://github.com/galaxyproject/galaxy/commit/50e596fb1b540a69f785296921a2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- reorder sections, un-quote bitbucket paragraph Commit: 9d5bf7b62d8f9a58e35e0317acb9dd5d88311b6f https://github.com/galaxyproject/galaxy/commit/9d5bf7b62d8f9a58e35e0317acb9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- minor release notes touch Commit: f887c059a2aff33a7c449d8ea234c4bbd9d09dd7 https://github.com/galaxyproject/galaxy/commit/f887c059a2aff33a7c449d8ea234… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- Expand 16.04 highlights... Commit: 8195d81739540ba489828616baa28a7b1c9d7711 https://github.com/galaxyproject/galaxy/commit/8195d81739540ba489828616baa2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M doc/source/releases/16.01.rst A doc/source/releases/16.04.rst M doc/source/releases/16.04_announce.rst A doc/source/releases/16.07_announce.rst M doc/source/releases/index.rst Log Message: ----------- Merge pull request #2353 from martenson/16.04_release_notes [16.04] Release notes for 16.04 Commit: 938e0c022063db0bc999d7699ae122e415452f34 https://github.com/galaxyproject/galaxy/commit/938e0c022063db0bc999d7699ae1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M doc/source/releases/16.01.rst A doc/source/releases/16.04.rst M doc/source/releases/16.04_announce.rst A doc/source/releases/16.07_announce.rst M doc/source/releases/index.rst M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge branch 'release_16.04' into dev Commit: 99c8f54a77c436125359f17a8d681f115e157742 https://github.com/galaxyproject/galaxy/commit/99c8f54a77c436125359f17a8d68… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 16.04 Commit: d03ba68ecf02ce7c352e43dedade111fed588bf6 https://github.com/galaxyproject/galaxy/commit/d03ba68ecf02ce7c352e43dedade… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Log Message: ----------- Merge branch 'release_16.04' into dev Commit: 5a15bd0a00a634d0856dca8bec8c7b78a6034dd4 https://github.com/galaxyproject/galaxy/commit/5a15bd0a00a634d0856dca8bec8c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M doc/source/releases/16.01.rst A doc/source/releases/16.04.rst M doc/source/releases/16.04_announce.rst A doc/source/releases/16.07_announce.rst M doc/source/releases/index.rst M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #2371 from jmchilton/dev Merge v16.04 into dev Compare: https://github.com/galaxyproject/galaxy/compare/a144a32f403b...5a15bd0a00a6

1 0

[galaxyproject/galaxy]
by GitHub 18 May '16

18 May '16

Branch: refs/tags/v16.04 Home: https://github.com/galaxyproject/galaxy

1 0

[galaxyproject/galaxy] 99c8f5: Update version to 16.04
by GitHub 18 May '16

18 May '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 99c8f54a77c436125359f17a8d681f115e157742 https://github.com/galaxyproject/galaxy/commit/99c8f54a77c436125359f17a8d68… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 16.04

1 0

[galaxyproject/galaxy] d8430e: generated notes with basic manual curation
by GitHub 18 May '16

18 May '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: d8430e5c4b6c5d8dd18fed6846f6f30d4a97e0eb https://github.com/galaxyproject/galaxy/commit/d8430e5c4b6c5d8dd18fed6846f6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: A doc/source/releases/16.04.rst M doc/source/releases/16.04_announce.rst A doc/source/releases/16.07_announce.rst M doc/source/releases/index.rst Log Message: ----------- generated notes with basic manual curation Commit: 93d1d5611e3d62f928af49edd884dfea5fcf4c11 https://github.com/galaxyproject/galaxy/commit/93d1d5611e3d62f928af49edd884… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- add deprecation notices Commit: 40e596f26479e14b66b71842cee779e46a882047 https://github.com/galaxyproject/galaxy/commit/40e596f26479e14b66b71842cee7… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- Update 16.04_announce.rst Added more deprecations from #1757 Commit: 86127cdfdd7140e167a54622b83e09e616dbbe9a https://github.com/galaxyproject/galaxy/commit/86127cdfdd7140e167a54622b83e… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- Update 16.04_announce.rst Fix my rst syntax. Commit: e0a9efc307ac9f3a7a36c724684b16802cd6d31b https://github.com/galaxyproject/galaxy/commit/e0a9efc307ac9f3a7a36c724684b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M doc/source/releases/16.04.rst M doc/source/releases/16.04_announce.rst Log Message: ----------- include security note for hg upgrade; some reordering Commit: edbc82c215e87a5962ed740d97c352931b9402c0 https://github.com/galaxyproject/galaxy/commit/edbc82c215e87a5962ed740d97c3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- Merge branch '16.04_release_notes' of https://github.com/martenson/galaxy into 16.04_release_notes Conflicts: doc/source/releases/16.04_announce.rst Commit: 633162c7f558f1bc3bfaaa54dde3c7fc4156c190 https://github.com/galaxyproject/galaxy/commit/633162c7f558f1bc3bfaaa54dde3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- fix wrong merge Commit: 65e1d68efd2a1bc83e340a8419f55f95a440c6c3 https://github.com/galaxyproject/galaxy/commit/65e1d68efd2a1bc83e340a8419f5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- typo Commit: db5c0d95f6e10a5a723bc4bb54c11597ed629e9c https://github.com/galaxyproject/galaxy/commit/db5c0d95f6e10a5a723bc4bb54c1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M doc/source/releases/16.04.rst Log Message: ----------- reorde notes a bit more based on impact/importance Commit: b85d604e30809d7e6b73f4762189182e7e82416b https://github.com/galaxyproject/galaxy/commit/b85d604e30809d7e6b73f4762189… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-13 (Fri, 13 May 2016) Changed paths: M doc/source/releases/16.01.rst M doc/source/releases/16.04.rst Log Message: ----------- Move some PRs that were merged in 16.01 before its release Galaxy 16.01 was officially released on 2016/02/24. Commit: c516c9fd45ffda5d4d74497bc96efc51966fdd22 https://github.com/galaxyproject/galaxy/commit/c516c9fd45ffda5d4d74497bc96e… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-13 (Fri, 13 May 2016) Changed paths: M doc/source/releases/16.04.rst Log Message: ----------- Fix truncated PR titles and some acknowledgements Commit: dc5a5eb2eb1af48e14234d42aa8cacd3fd1aba1e https://github.com/galaxyproject/galaxy/commit/dc5a5eb2eb1af48e14234d42aa8c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-13 (Fri, 13 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- Add Bitbucket deprecation details Commit: 76fb9b72c34ecd6bead61b372a32dc0bd24375eb https://github.com/galaxyproject/galaxy/commit/76fb9b72c34ecd6bead61b372a32… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-13 (Fri, 13 May 2016) Changed paths: M doc/source/releases/16.04.rst Log Message: ----------- Add some missing PRs and merge some entries Commit: 3b7f6cb7777cf2a92d17928b38abe13bd3cdb338 https://github.com/galaxyproject/galaxy/commit/3b7f6cb7777cf2a92d17928b38ab… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- add some highlights, seems tough for this release Commit: 62b6eaa92aac9520f12968cb41690692c8c3fa4f https://github.com/galaxyproject/galaxy/commit/62b6eaa92aac9520f12968cb4169… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M doc/source/releases/16.01.rst M doc/source/releases/16.04.rst M doc/source/releases/16.04_announce.rst Log Message: ----------- Merge branch '16.04_release_notes' of https://github.com/martenson/galaxy into 16.04_release_notes Commit: afb9027482f3a98a2b6d9e9fd049ded1da78c666 https://github.com/galaxyproject/galaxy/commit/afb9027482f3a98a2b6d9e9fd049… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- final touch of release notes from my side Commit: 50e596fb1b540a69f785296921a2611566a5b12b https://github.com/galaxyproject/galaxy/commit/50e596fb1b540a69f785296921a2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- reorder sections, un-quote bitbucket paragraph Commit: 9d5bf7b62d8f9a58e35e0317acb9dd5d88311b6f https://github.com/galaxyproject/galaxy/commit/9d5bf7b62d8f9a58e35e0317acb9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- minor release notes touch Commit: f887c059a2aff33a7c449d8ea234c4bbd9d09dd7 https://github.com/galaxyproject/galaxy/commit/f887c059a2aff33a7c449d8ea234… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M doc/source/releases/16.04_announce.rst Log Message: ----------- Expand 16.04 highlights... Commit: 8195d81739540ba489828616baa28a7b1c9d7711 https://github.com/galaxyproject/galaxy/commit/8195d81739540ba489828616baa2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-18 (Wed, 18 May 2016) Changed paths: M doc/source/releases/16.01.rst A doc/source/releases/16.04.rst M doc/source/releases/16.04_announce.rst A doc/source/releases/16.07_announce.rst M doc/source/releases/index.rst Log Message: ----------- Merge pull request #2353 from martenson/16.04_release_notes [16.04] Release notes for 16.04 Compare: https://github.com/galaxyproject/galaxy/compare/cc86096c83b5...8195d8173954

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[galaxyproject/galaxy] 365f4b: modifying getIndex method
by GitHub 17 May '16

17 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 365f4b374e3af4134b57144e9340676ac4f903a5 https://github.com/galaxyproject/galaxy/commit/365f4b374e3af4134b57144e9340… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select.js Log Message: ----------- modifying getIndex method Commit: b361ffa1c217a7e2c57a4d770b100ec718ca22b8 https://github.com/galaxyproject/galaxy/commit/b361ffa1c217a7e2c57a4d770b10… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select.js M static/maps/mvc/ui/ui-select.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select.js Log Message: ----------- removing old code from _getIndex method Commit: 7f95786aef314a9484a5dab78d2883d9d42a8a43 https://github.com/galaxyproject/galaxy/commit/7f95786aef314a9484a5dab78d28… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M client/bower.json M client/galaxy/scripts/mvc/ui/ui-select.js M static/maps/mvc/ui/ui-select.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select.js Log Message: ----------- Adding latest Underscore.js dependency Commit: e96b8bbf7afcfc58162b599a0e3d4e3d1fd0755a https://github.com/galaxyproject/galaxy/commit/e96b8bbf7afcfc58162b599a0e3d… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M CONTRIBUTORS.md M Makefile M client/README.md M client/bower.json M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/libs/backbone.js M client/galaxy/scripts/libs/bootstrap-tour.js M 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lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/utility_containers/__init__.py M lib/tool_shed/utility_containers/utility_container_manager.py M static/maps/layout/page.js.map M static/maps/libs/backbone.js.map M static/maps/libs/bootstrap-tour.js.map M static/maps/libs/d3.js.map M static/maps/libs/jquery/jquery.js.map M static/maps/libs/jquery/jquery.migrate.js.map M static/maps/libs/raven.js.map M static/maps/libs/require.js.map M static/maps/libs/tracekit.js.map M static/maps/libs/underscore.js.map M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-annotated.js.map M 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static/maps/utils/metrics-logger.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js M static/scripts/libs/backbone.js M static/scripts/libs/bootstrap-tour.js M static/scripts/libs/d3.js M static/scripts/libs/jquery/jquery.js M static/scripts/libs/jquery/jquery.migrate.js M static/scripts/libs/raven.js M static/scripts/libs/require.js M static/scripts/libs/tracekit.js M static/scripts/libs/underscore.js M static/scripts/mvc/citation/citation-model.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/ui/popup-menu.js M static/scripts/mvc/ui/ui-drilldown.js M static/scripts/mvc/ui/ui-list.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-options.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/ui/ui-select.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/ui/hoverhighlight.js M static/scripts/ui/loading-indicator.js M static/scripts/ui/mode-button.js M static/scripts/ui/pagination.js M static/scripts/ui/peek-column-selector.js M static/scripts/utils/localization.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/utils.js M static/style/blue/base.css M templates/base/base_panels.mako M templates/display_base.mako M templates/sharing_base.mako M templates/show_params.mako A templates/slug_editing_js.mako M templates/webapps/galaxy/data_manager/view_job.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/library/common/browse_library.mako M templates/webapps/galaxy/library/common/ldda_info.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/run.mako M templates/webapps/galaxy/workflow/sharing.mako M templates/webapps/tool_shed/index.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/manage_repository.mako M test/api/test_tools.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/interface.py M test/api/workflows_format_2/main.py M test/base/interactor.py A test/functional/tools/multi_data_repeat.xml M test/functional/tools/samples_tool_conf.xml M test/integration/test_pulsar_embedded.py M test/qunit/test-common.js R test/qunit/test-libs/qunit-1.14.0.css R test/qunit/test-libs/qunit-1.14.0.js A test/qunit/test-libs/qunit-1.23.1.css A test/qunit/test-libs/qunit-1.23.1.js A test/qunit/test-libs/sinon-1.17.3.js R test/qunit/test-libs/sinon-1.9.1.js M test/qunit/tests/form_tests.js M test/qunit/tests/list-of-pairs-collection-creator.js M test/qunit/tests/metrics-logger.js M test/qunit/tests/page_tests.js M test/qunit/tests/ui_tests.html M test/qunit/tests/ui_tests.js A test/qunit/tests/utils_test.html A test/qunit/tests/utils_test.js M test/qunit/tests/workflow_editor_tests.js R test/shed_functional/functional/test_0450_skip_tool_tests.py M test/shed_functional/functional/test_0540_get_all_metadata_from_api.py A test/shed_functional/functional/test_0550_metadata_updated_dependencies.py A test/shed_functional/test_data/0550_files/filtering_1.0.tgz A test/shed_functional/test_data/0550_files/package_freebayes_1_0550.tgz A test/shed_functional/test_data/0550_files/package_freebayes_2_0550.tgz A test/shed_functional/test_data/0550_files/package_samtools_1_0550.tgz A test/shed_functional/test_data/0550_files/package_samtools_2_0550.tgz A test/shed_functional/test_data/0550_files/temp/tool_dependencies.xml M test/unit/test_objectstore.py M tools/data_source/biomart.xml M tools/data_source/upload.py M tools/filters/trimmer.xml M tools/stats/grouping.py M tools/stats/grouping.xml Log Message: ----------- Adding changes for latest Underscore JS library Commit: 4d6b8bf2b44a96d97b98fbc992ffc8518acb6a82 https://github.com/galaxyproject/galaxy/commit/4d6b8bf2b44a96d97b98fbc992ff… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M client/bower.json Log Message: ----------- reverting the version of underscore as it is already updated in the galaxy main Commit: a144a32f403bad299793a494e0547483c5cb1322 https://github.com/galaxyproject/galaxy/commit/a144a32f403bad299793a494e054… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select.js M static/maps/mvc/ui/ui-select.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select.js Log Message: ----------- Merge branch 'dev' of https://github.com/anuprulez/galaxy into anuprulez-dev Conflicts: static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map Compare: https://github.com/galaxyproject/galaxy/compare/c2ea4ee52663...a144a32f403b

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[galaxyproject/infrastructure-playbook] 5763b3: Modify Jetstream access lists
by GitHub 17 May '16

17 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 5763b32749635d5db46e8d61ae9afac7bb1347cb https://github.com/galaxyproject/infrastructure-playbook/commit/5763b327496… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: A common_env/secret_group_vars/baseenv.yml A jetstreamiuenv/secret_group_vars/baseenv.yml A jetstreamiuenv/secret_group_vars/controllers.yml A jetstreamtaccenv/secret_group_vars/baseenv.yml A jetstreamtaccenv/secret_group_vars/controllers.yml Log Message: ----------- Modify Jetstream access lists

1 0